quarta-feira, julho 31, 2013

Edited by Steven M. Stanley, University of Hawaii, Honolulu, HI, and approved May 15, 2013 (received for review February 9, 2013)

Abstract

There are few putative macroevolutionary trends or rules that withstand scrutiny. Here, we test and verify the purported tendency for animal clades to reach their maximum morphological variety relatively early in their evolutionary histories (early high disparity). We present a meta-analysis of 98 metazoan clades radiating throughout the Phanerozoic. The disparity profiles of groups through time are summarized in terms of their center of gravity (CG), with values above and below 0.50 indicating top- and bottom-heaviness, respectively. Clades that terminate at one of the “big five” mass extinction events tend to have truncated trajectories, with a significantly top-heavy CG distribution overall. The remaining 63 clades show the opposite tendency, with a significantly bottom-heavy mean CG (relatively early high disparity). Resampling tests are used to identify groups with a CG significantly above or below 0.50; clades not terminating at a mass extinction are three times more likely to be significantly bottom-heavy than top-heavy. Overall, there is no clear temporal trend in disparity profile shapes from the Cambrian to the Recent, and early high disparity is the predominant pattern throughout the Phanerozoic. Our results do not allow us to distinguish between ecological and developmental explanations for this phenomenon. To the extent that ecology has a role, however, the paucity of bottom-heavy clades radiating in the immediate wake of mass extinctions suggests that early high disparity more probably results from the evolution of key apomorphies at the base of clades rather than from physical drivers or catastrophic ecospace clearing.

Changes in gene expression have been proposed to have an important role in the evolutionary changes in phenotypes. Interspecific changes in gene expression can result not only from genetic changes in regulatory regions but also from epigenetic changes in such regions. Here we report the identification of genomic regions showing differences in DNA methylation between humans and chimpanzees (termed S-DMRs for species-specific differentially methylated regions) on chromosomes 21 and 22. These regional methylation differences are frequently associated with genes, including those relevant to a disease, such as Alzheimer’s disease, diabetes mellitus or cancer. Methylation differences are often correlated with changes in promoter activity or alternative splicing. Comparative studies including other great ape species provide evidence for the contribution of genetic changes to some of these S-DMRs. Genetic changes responsible for the S-DMRs include gain or loss of CTCF-binding site and changes in CpG density in microsatellite repeats. Our results suggest that DNA methylation changes, often caused by small sequence changes, contribute to transcriptional and phenotypic diversification in hominid evolution.

“The work reveals that some conventional boundaries between the kingdoms of life are not as rigid as has been thought. For instance, the researchers suggest that one bacterial lineage synthesizes purine bases — building blocks of DNA and RNA — using enzymes previously thought to exist only in archaea. Meanwhile, three of the archaeal cells sequenced in the study harbour sigma factors, which initiate RNA transcription and have previously been found only in bacteria.”

“The researchers also found a bacterium that has ‘recoded’ the three-letter series of bases UGA — known as the opal stop codon. In almost every other organism, this nucleotide sequence signals the cell to stop translating RNA into protein. But in this organism, it tells the cell to make the amino acid glycine. The team propose to place it into a new bacterial phylum, called Gracilibacteria.”

Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called ‘microbial dark matter’. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of lie and provides a systematic step towards a better understanding of biological evolution on our planet.

Received 14 January 2013 Accepted 04 June 2013 Published online 14 July 2013

We present design and first demonstration of optics for a telescopic contact lens with independent optical paths for switching between normal and magnified vision. The magnified optical path incorporates a telescopic arrangement of positive and negative annular concentric reflectors to achieve 2.8x magnification on the eye, while light passing through a central clear aperture provides unmagnified vision. We present an experimental demonstration of the contact lens mounted on a life-sized optomechanical model eye and, using a pair of modified commercial 3D television glasses, demonstrate electrically operated polarization switching between normal and magnified vision.

"This highlights a further issue of confusion often prevalent among scientists and that politicians often perpetuate when challenged--the belief that all decisions need to be evidence-based. My experience is that most policy decisions are informed to greater or lesser degrees by evidence but rarely is it practical or even desirable to base decisions entirely upon scientific evidence. THE WORLD DOES NOT STOP AT THE POINT WHERE SCIENTIFIC CERTAINTY ENDS, and those implementing policy usually have no choice but to continue making decisions and implementing actions when there is scientific uncertainty.

This perhaps represents the greatest disparity between the aspirations of scientists and the reality faced by policy-makers. Moreover, the clarion call from scientists 'we need to do more research' is guaranteed to boil the blood of some policy-makers, especially when past investment in science has, if anything, added to the level of apparent scientific uncertainty. THE INTEGRITY OF SCIENCE STARTS TO BE UNDERMINED WHEN SCIENTISTS THEMSELVES SUGGEST THAT THE GREY AREA OF UNCERTAINTY SHOULD BE OCCUPIED BY THEM ALONE rather than being shared with those implementing policy. This has happened in many of the most controversial areas in my portfolio including bovine TB, pesticides and marine management."

segunda-feira, julho 01, 2013

Lateral Gene Transfer, Rearrangement and Reconciliation

Murray Patterson, Gergely J Szöllősi, Vincent Daubin, Eric Tannier

(Submitted on 27 Jun 2013)

Background.

Models of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via reconciled gene trees. In unicellular organisms, these models have so far ignored lateral gene transfer, even though it can have an important confounding effect on such models, as well as a rich source of information on the function of genes through the detection of transfers of entire clusters of genes.

Result.

We report an algorithm together with its implementation, DeCoLT, that reconstructs ancestral genome organization based on reconciled gene trees which summarize information on sequence evolution, gene origination, duplication, loss, and lateral transfer. DeCoLT finds in polynomial time the minimum number of rearrangements, computed as the number of gains and breakages of adjacencies between pairs of genes. We apply DeCoLT to 1099 gene families from 36 cyanobacteria genomes.

Conclusion.

DeCoLT is able to reconstruct adjacencies in 35 ancestral bacterial genomes with a thousand genes families in a few hours, and detects clusters of co-transferred genes. As there is no constraint on genome organization, adjacencies can be generalized to any relationship between genes to reconstruct ancestral interactions, functions or complexes with the same framework.

The existence of Hesperian age (3.7–3.4 Ga) surface water bodies on Mars is a contentious issue, often conflicting with favored climate models. Extensive lakes are proposed to have filled parts of Valles Marineris during this period, yet evidence for their presence and temporal continuity is poorly constrained. Here we report geomorphic and chronologic evidence for the initiation and demise of a voluminous lake system within the basins of eastern Valles Marineris. We find that independent, kilometer-deep lakes were present here well after the wetter, global climate optimum that characterized the previous Noachian epoch (4.1–3.7 Ga). Relative and impact crater chronologies of flood channels emerging from lake basins indicate relatively late lake spillover in the Early Amazonian (ca. 3.0 Ga). Drawdown of the lake and cessation of interbasin sedimentation may be recorded by a similar Early Amazonian (ca. 3.1 Ga) crater retention age on the surface of Capri Mensa, a 4-km-tall, sulfate-bearing interior layered deposit. The topography data demonstrate that incision of the bedrock barriers between the basins during spillover was driven by a dramatic local base-level difference between the lake surface and downstream basin floors. We postulate that the lake spillover process created an integrated drainage routing system between a voluminous equatorial water supply and the northern plains basin.

Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved January 17, 2013 (received for review December 2, 2012)

Abstract

In the last two decades, the widespread application of genetic and genomic approaches has revealed a bacterial world astonishing in its ubiquity and diversity.This review examines how a growing knowledge of the vast range of animal–bacterial interactions, whether in shared ecosystems or intimate symbioses, is fundamentally altering our understanding of animal biology.Specifically, we highlight recent technological and intellectual advances that have changed our thinking about five questions: how have bacteria facilitated the origin and evolution of animals; how do animals and bacteria affect each other’s genomes; how does normal animal development depend on bacterial partners; how is homeostasis maintained between animals and their symbionts; and how can ecological approaches deepen our understanding of the multiple levels of animal–bacterial interaction.As answers to these fundamental questions emerge, all biologists will be challenged to broaden their appreciation of these interactions and to include investigations of the relationships between and among bacteria and their animal partners as we seek a better understanding of the natural world.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Background

Recent advances in genomics of viruses and cellular life forms have greatly stimulated interest in the origins and evolution of viruses and, for the first time, offer an opportunity for a data-driven exploration of the deepest roots of viruses. Here we briefly review the current views of virus evolution and propose a new, coherent scenario that appears to be best compatible with comparative-genomic data and is naturally linked to models of cellular evolution that, from independent considerations, seem to be the most parsimonious among the existing ones.

Results

Several genes coding for key proteins involved in viral replication and morphogenesis as well as the major capsid protein of icosahedral virions are shared by many groups of RNA and DNA viruses but are missing in cellular life forms. On the basis of this key observation and the data on extensive genetic exchange between diverse viruses, we propose the concept of the ancient virus world. The virus world is construed as a distinct contingent of viral genes that continuously retained its identity throughout the entire history of life. Under this concept, the principal lineages of viruses and related selfish agents emerged from the primordial pool of primitive genetic elements, the ancestors of both cellular and viral genes. Thus, notwithstanding the numerous gene exchanges and acquisitions attributed to later stages of evolution, most, if not all, modern viruses and other selfish agents are inferred to descend from elements that belonged to the primordial genetic pool. In this pool, RNA viruses would evolve first, followed by retroid elements, and DNA viruses. The Virus World concept is predicated on a model of early evolution whereby emergence of substantial genetic diversity antedates the advent of full-fledged cells, allowing for extensive gene mixing at this early stage of evolution. We outline a scenario of the origin of the main classes of viruses in conjunction with a specific model of precellular evolution under which the primordial gene pool dwelled in a network of inorganic compartments. Somewhat paradoxically, under this scenario, we surmise that selfish genetic elements ancestral to viruses evolved prior to typical cells, to become intracellular parasites once bacteria and archaea arrived at the scene. Selection against excessively aggressive parasites that would kill off the host ensembles of genetic elements would lead to early evolution of temperate virus-like agents and primitive defense mechanisms, possibly, based on the RNA interference principle. The emergence of the eukaryotic cell is construed as the second melting pot of virus evolution from which the major groups of eukaryotic viruses originated as a result of extensive recombination of genes from various bacteriophages, archaeal viruses, plasmids, and the evolving eukaryotic genomes. Again, this vision is predicated on a specific model of the emergence of eukaryotic cell under which archaeo-bacterial symbiosis was the starting point of eukaryogenesis, a scenario that appears to be best compatible with the data.

Conclusion

The existence of several genes that are central to virus replication and structure, are shared by a broad variety of viruses but are missing from cellular genomes (virus hallmark genes) suggests the model of an ancient virus world, a flow of virus-specific genes that went uninterrupted from the precellular stage of life's evolution to this day. This concept is tightly linked to two key conjectures on evolution of cells: existence of a complex, precellular, compartmentalized but extensively mixing and recombining pool of genes, and origin of the eukaryotic cell by archaeo-bacterial fusion. The virus world concept and these models of major transitions in the evolution of cells provide complementary pieces of an emerging coherent picture of life's history.